The major goal of this proposal is the development of an automated system for DNA sequence analysis. The system, based upon the shotgun strategy, will be developed in three phases, in which successively greater fractions of the sequencing process are automated. In Phase I the steps of sequencing reaction performance, sequencing reaction purification, gel loading, electrophoresis, and data analysis will be automated in an integrated format. In Phase II the system will be extended to include plaque picking, bacterial cell culture and template purification. In Phase III a limiting dilution front-end strategy for clonal isolation will be incorporated. Thus by the end of Phase III the system will automate all aspects of shotgun sequencing subsequent to the transformation of bacterial cells with recombinant DNA molecules (library construction). The projected operating cost at a throughput of 300,000 bases raw data (20 kb finished data in the worst-case scenario) per day is about $0.15/base finished data. This system will require two persons for operation.